Filtered
#Calculate Hill numbers
richness <- genome_counts_filt %>%
column_to_rownames(var="genome") %>%
select(where(~!all(. == 0))) %>%
hilldiv(.,q=0) %>%
t() %>%
as.data.frame() %>%
rename(richness=1) %>%
rownames_to_column(var="microsample")
neutral <- genome_counts_filt %>%
column_to_rownames(var="genome") %>%
select(where(~!all(. == 0))) %>%
hilldiv(.,q=1) %>%
t() %>%
as.data.frame() %>%
rename(neutral=1) %>%
rownames_to_column(var="microsample")
phylogenetic <- genome_counts_filt %>%
column_to_rownames(var="genome") %>%
select(where(~!all(. == 0))) %>%
hilldiv(.,q=1,tree=genome_tree) %>%
t() %>%
as.data.frame() %>%
rename(phylogenetic=1) %>%
rownames_to_column(var="microsample")
# Merge alpha diversities
alpha_diversity <- richness %>%
full_join(neutral,by=join_by(microsample==microsample)) %>%
full_join(phylogenetic,by=join_by(microsample==microsample)) %>%
left_join(sample_metadata, by=join_by(microsample==microsample))
# Write alpha diversities
alpha_diversity %>% write_tsv("results/alpha_div_filtered.tsv")
# Print alpha diversity
alpha_diversity %>%
select(microsample,richness, neutral, phylogenetic, section, buffer, batch, protocol, Xcoord, Ycoord, size) %>%
tt()
tinytable_3wl4v01hew03pqzahdch
| microsample |
richness |
neutral |
phylogenetic |
section |
buffer |
batch |
protocol |
Xcoord |
Ycoord |
size |
| M300554 |
105 |
45.801912 |
3.911416 |
Caecum right |
B11 |
MSEB0006 |
full_ulv2 |
74953.325 |
27445.67 |
4976 |
| M300555 |
3 |
2.654441 |
1.657236 |
Caecum right |
B11 |
MSEB0006 |
full_ulv2 |
72020.280 |
33695.14 |
4976 |
| M300556 |
3 |
2.921247 |
1.813378 |
Caecum right |
B11 |
MSEB0006 |
full_ulv2 |
75415.387 |
27819.35 |
4976 |
| M300557 |
81 |
43.169579 |
3.712575 |
Caecum right |
B11 |
MSEB0006 |
full_ulv2 |
76113.477 |
28351.85 |
4976 |
| M300559 |
105 |
46.235275 |
3.924148 |
Caecum right |
B11 |
MSEB0006 |
full_ulv2 |
76849.228 |
29025.05 |
4976 |
| M300560 |
99 |
44.437305 |
4.065477 |
Caecum right |
B11 |
MSEB0006 |
full_ulv2 |
75971.705 |
29352.86 |
4976 |
| M300561 |
103 |
44.311493 |
4.092159 |
Caecum right |
B11 |
MSEB0006 |
full_ulv2 |
76680.937 |
29558.16 |
4976 |
| M300562 |
103 |
46.882732 |
4.021131 |
Caecum right |
B11 |
MSEB0006 |
full_ulv2 |
74883.318 |
29170.18 |
5140 |
| M300563 |
109 |
47.059960 |
3.989914 |
Caecum right |
B11 |
MSEB0006 |
full_ulv2 |
75220.992 |
29120.51 |
5140 |
| M300564 |
12 |
10.477468 |
2.957506 |
Caecum right |
B11 |
MSEB0006 |
full_ulv2 |
75894.617 |
29134.86 |
5140 |
| M300566 |
93 |
43.059847 |
3.761573 |
Caecum right |
B11 |
MSEB0006 |
full_ulv2 |
76922.541 |
29224.45 |
5140 |
| M300567 |
99 |
44.029116 |
4.012374 |
Caecum right |
B11 |
MSEB0006 |
full_ulv2 |
77492.203 |
29097.78 |
5140 |
| M300569 |
100 |
46.805777 |
4.101282 |
Caecum right |
B11 |
MSEB0006 |
full_ulv2 |
77495.465 |
28977.76 |
5140 |
| M300570 |
100 |
44.462204 |
3.951953 |
Caecum right |
B11 |
MSEB0006 |
full_ulv2 |
74950.841 |
28473.11 |
4815 |
| M300571 |
94 |
42.482781 |
3.877417 |
Caecum right |
B11 |
MSEB0006 |
full_ulv2 |
75619.946 |
28632.40 |
4815 |
| M300572 |
56 |
32.680577 |
3.739918 |
Caecum right |
B11 |
MSEB0006 |
full_ulv2 |
76345.933 |
29031.81 |
4815 |
| M300574 |
97 |
43.914978 |
3.965100 |
Caecum right |
B11 |
MSEB0006 |
full_ulv2 |
76920.997 |
29347.99 |
4815 |
| M300576 |
92 |
43.158898 |
3.953223 |
Caecum right |
B11 |
MSEB0006 |
full_ulv2 |
77104.532 |
29588.79 |
4815 |
| M300577 |
103 |
44.666492 |
3.976265 |
Caecum right |
B11 |
MSEB0006 |
full_ulv2 |
77418.895 |
29907.92 |
4815 |
| M300578 |
101 |
44.526067 |
3.915702 |
Caecum right |
B12 |
MSEB0006 |
full_ulv2 |
76897.212 |
30198.48 |
5140 |
| M300580 |
102 |
43.777961 |
3.939951 |
Caecum right |
B12 |
MSEB0006 |
full_ulv2 |
77026.940 |
30039.53 |
5140 |
| M300581 |
79 |
39.975639 |
3.872346 |
Caecum right |
B12 |
MSEB0006 |
full_ulv2 |
77028.597 |
29718.20 |
5140 |
| M300582 |
78 |
38.898531 |
3.881888 |
Caecum right |
B12 |
MSEB0006 |
full_ulv2 |
77019.213 |
29448.24 |
5140 |
| M300583 |
95 |
38.373844 |
3.975637 |
Caecum right |
B12 |
MSEB0006 |
full_ulv2 |
77009.202 |
28923.10 |
5140 |
| M300584 |
104 |
44.918626 |
3.965482 |
Caecum right |
B12 |
MSEB0006 |
full_ulv2 |
77019.413 |
28061.84 |
5140 |
| M300588 |
102 |
42.618728 |
3.970993 |
Caecum right |
B12 |
MSEB0006 |
full_ulv2 |
75330.017 |
26890.36 |
5141 |
| M300589 |
99 |
41.459691 |
3.936518 |
Caecum right |
B12 |
MSEB0006 |
full_ulv2 |
75862.866 |
27323.96 |
5141 |
| M300590 |
96 |
40.482162 |
4.103071 |
Caecum right |
B12 |
MSEB0006 |
full_ulv2 |
76508.231 |
27653.84 |
5141 |
| M300592 |
103 |
40.971234 |
4.064549 |
Caecum right |
B12 |
MSEB0006 |
full_ulv2 |
77351.464 |
28017.27 |
5141 |
| M300593 |
98 |
42.126550 |
4.054750 |
Caecum right |
B12 |
MSEB0006 |
full_ulv2 |
77854.216 |
28261.49 |
5141 |
| M300594 |
96 |
43.659879 |
4.039384 |
Caecum right |
B12 |
MSEB0006 |
full_ulv2 |
75509.650 |
26477.82 |
4976 |
| M300595 |
102 |
37.738766 |
4.048987 |
Caecum right |
B12 |
MSEB0006 |
full_ulv2 |
75650.540 |
26591.91 |
4976 |
| M300596 |
105 |
40.160724 |
4.033115 |
Caecum right |
B12 |
MSEB0006 |
full_ulv2 |
75822.838 |
26598.11 |
4976 |
| M300597 |
100 |
40.582505 |
4.079831 |
Caecum right |
B12 |
MSEB0006 |
full_ulv2 |
76147.102 |
26625.28 |
4976 |
| M300598 |
101 |
41.887011 |
4.025419 |
Caecum right |
B12 |
MSEB0006 |
full_ulv2 |
76899.245 |
26623.52 |
4976 |
| M300599 |
104 |
42.932100 |
3.943969 |
Caecum right |
B12 |
MSEB0006 |
full_ulv2 |
76852.725 |
26643.02 |
4976 |
| M300602 |
4 |
3.258694 |
1.446601 |
Ileum |
B11 |
MSEB0006 |
full_ulv2 |
104424.700 |
42749.48 |
5140 |
| M300603 |
3 |
2.026603 |
1.264579 |
Ileum |
B11 |
MSEB0006 |
full_ulv2 |
104606.900 |
42459.54 |
5140 |
| M300605 |
2 |
1.729081 |
1.214454 |
Ileum |
B11 |
MSEB0006 |
full_ulv2 |
104954.500 |
42730.89 |
5140 |
| M300606 |
1 |
1.000000 |
1.000000 |
Ileum |
B11 |
MSEB0006 |
full_ulv2 |
105122.500 |
42666.74 |
5140 |
| M300608 |
4 |
2.614424 |
1.427086 |
Ileum |
B11 |
MSEB0006 |
full_ulv2 |
105262.700 |
42589.77 |
5140 |
| M300609 |
4 |
3.096111 |
1.455646 |
Ileum |
B11 |
MSEB0006 |
full_ulv2 |
105328.900 |
42703.60 |
5140 |
| M300610 |
4 |
3.092445 |
1.478474 |
Ileum |
B11 |
MSEB0006 |
full_ulv2 |
105102.400 |
41497.10 |
4976 |
| M300611 |
1 |
1.000000 |
1.000000 |
Ileum |
B11 |
MSEB0006 |
full_ulv2 |
105146.000 |
41596.22 |
4976 |
| M300612 |
4 |
3.200070 |
1.466971 |
Ileum |
B11 |
MSEB0006 |
full_ulv2 |
105281.000 |
41702.52 |
4976 |
| M300613 |
1 |
1.000000 |
1.000000 |
Ileum |
B11 |
MSEB0006 |
full_ulv2 |
105408.300 |
41533.66 |
4976 |
| M300616 |
3 |
1.602470 |
1.192713 |
Ileum |
B11 |
MSEB0006 |
full_ulv2 |
105595.700 |
41999.37 |
4976 |
| M300617 |
4 |
2.597621 |
1.410566 |
Ileum |
B11 |
MSEB0006 |
full_ulv2 |
105983.000 |
42106.21 |
4976 |
| M300619 |
3 |
1.859573 |
1.237721 |
Ileum |
B11 |
MSEB0006 |
full_ulv2 |
106845.700 |
41525.80 |
5306 |
| M300622 |
3 |
2.658765 |
1.353273 |
Ileum |
B11 |
MSEB0006 |
full_ulv2 |
107262.300 |
42133.87 |
5306 |
| M300623 |
3 |
2.873136 |
1.380176 |
Ileum |
B11 |
MSEB0006 |
full_ulv2 |
107820.600 |
41925.02 |
5306 |
| M300624 |
1 |
1.000000 |
1.000000 |
Ileum |
B11 |
MSEB0006 |
full_ulv2 |
107233.500 |
41764.35 |
5306 |
| M300627 |
3 |
2.862931 |
1.378919 |
Ileum |
B12 |
MSEB0006 |
full_ulv2 |
108112.000 |
45420.81 |
4815 |
| M300628 |
4 |
2.628829 |
1.499791 |
Ileum |
B12 |
MSEB0006 |
full_ulv2 |
108221.600 |
45346.45 |
4815 |
| M300629 |
4 |
1.907144 |
1.302185 |
Ileum |
B12 |
MSEB0006 |
full_ulv2 |
108085.500 |
45636.13 |
4815 |
| M300630 |
4 |
1.854313 |
1.280920 |
Ileum |
B12 |
MSEB0006 |
full_ulv2 |
108093.700 |
45848.93 |
4815 |
| M300631 |
5 |
3.608828 |
1.721713 |
Ileum |
B12 |
MSEB0006 |
full_ulv2 |
107697.500 |
45704.29 |
4815 |
| M300633 |
6 |
2.179216 |
1.433128 |
Ileum |
B12 |
MSEB0006 |
full_ulv2 |
107727.500 |
45487.09 |
4815 |
| M300634 |
5 |
2.654260 |
1.433183 |
Ileum |
B12 |
MSEB0006 |
full_ulv2 |
106635.900 |
42106.55 |
5384 |
| M300636 |
4 |
2.513021 |
1.484550 |
Ileum |
B12 |
MSEB0006 |
full_ulv2 |
106545.500 |
42220.70 |
5384 |
| M300638 |
4 |
2.712719 |
1.464181 |
Ileum |
B12 |
MSEB0006 |
full_ulv2 |
106647.000 |
42288.86 |
5384 |
| M300639 |
7 |
2.562594 |
1.486765 |
Ileum |
B12 |
MSEB0006 |
full_ulv2 |
106800.500 |
41821.88 |
5384 |
| M300640 |
3 |
2.025162 |
1.264308 |
Ileum |
B12 |
MSEB0006 |
full_ulv2 |
107052.700 |
42525.49 |
5384 |
| M300642 |
1 |
1.000000 |
1.000000 |
Ileum |
B12 |
MSEB0006 |
full_ulv2 |
108030.700 |
43599.50 |
4976 |
| M300644 |
5 |
1.600004 |
1.208205 |
Ileum |
B12 |
MSEB0006 |
full_ulv2 |
NA |
NA |
NA |
| M300645 |
5 |
1.502894 |
1.239684 |
Ileum |
B12 |
MSEB0006 |
full_ulv2 |
107988.200 |
43509.47 |
4976 |
| M300647 |
5 |
3.154388 |
1.457167 |
Ileum |
B12 |
MSEB0006 |
full_ulv2 |
107969.500 |
43138.84 |
4976 |
| M300648 |
5 |
1.758864 |
1.265810 |
Ileum |
B12 |
MSEB0006 |
full_ulv2 |
107883.700 |
43169.50 |
4976 |
| M300651 |
102 |
46.742684 |
3.929222 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
11906.706 |
17302.78 |
5140 |
| M300652 |
100 |
42.923634 |
4.114776 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
14050.460 |
17001.92 |
5140 |
| M300654 |
96 |
37.251363 |
3.830623 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
14807.470 |
19475.98 |
5140 |
| M300656 |
7 |
6.275011 |
2.411725 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
15095.242 |
18655.46 |
5140 |
| M300657 |
34 |
19.736256 |
3.557363 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
15154.326 |
19081.92 |
5140 |
| M300658 |
99 |
42.314901 |
4.036385 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
9192.814 |
19234.39 |
4976 |
| M300659 |
119 |
42.309365 |
3.994236 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
12511.076 |
19365.33 |
4976 |
| M300661 |
103 |
39.608207 |
3.905772 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
11699.514 |
20259.00 |
4976 |
| M300662 |
104 |
44.515529 |
3.819290 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
13804.910 |
20094.72 |
4976 |
| M300664 |
15 |
11.273184 |
3.132174 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
12513.988 |
21896.24 |
4976 |
| M300665 |
4 |
2.814786 |
1.704808 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
9669.578 |
19330.82 |
4976 |
| M300666 |
111 |
42.796930 |
3.995646 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
10924.656 |
21602.49 |
5384 |
| M300668 |
108 |
39.784202 |
3.977135 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
14208.788 |
22187.84 |
5384 |
| M300669 |
104 |
41.185041 |
4.089677 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
13658.990 |
21278.18 |
5384 |
| M300670 |
85 |
39.361771 |
3.851039 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
15752.910 |
20908.01 |
5384 |
| M300671 |
104 |
40.283873 |
4.066253 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
13086.410 |
21703.25 |
5384 |
| M300672 |
94 |
40.061994 |
3.858419 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
13311.294 |
20916.06 |
5384 |
| M300673 |
98 |
38.528300 |
4.029266 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
14520.766 |
22307.33 |
5384 |
| M300674 |
109 |
44.864962 |
3.943580 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
12054.270 |
23154.78 |
5051 |
| M300675 |
114 |
44.861236 |
3.939224 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
13501.846 |
20960.88 |
5051 |
| M300676 |
96 |
39.189195 |
4.028682 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
14952.726 |
23717.40 |
5051 |
| M300677 |
31 |
20.289760 |
3.183021 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
12773.380 |
21535.84 |
5051 |
| M300678 |
116 |
43.357715 |
3.994201 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
12504.528 |
21793.47 |
5051 |
| M300679 |
104 |
41.578976 |
3.992278 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
12589.016 |
20536.83 |
5051 |
| M300680 |
112 |
44.937212 |
4.032103 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
13215.834 |
22405.85 |
5051 |
| M300681 |
2 |
1.999637 |
1.764608 |
Caecum right |
B12 |
MSEB0009 |
full_celero |
NA |
NA |
NA |
| M300682 |
6 |
5.048966 |
2.842439 |
Caecum right |
B12 |
MSEB0009 |
half_ulv2 |
14464.852 |
18168.78 |
4976 |
| M300683 |
96 |
39.991157 |
4.070488 |
Caecum right |
B12 |
MSEB0009 |
half_ulv2 |
15660.538 |
17029.20 |
4976 |
| M300684 |
97 |
38.327913 |
3.983029 |
Caecum right |
B12 |
MSEB0009 |
half_ulv2 |
13001.740 |
18200.66 |
4976 |
| M300687 |
106 |
42.965867 |
3.998442 |
Caecum right |
B12 |
MSEB0009 |
half_ulv2 |
14317.052 |
18439.38 |
4976 |
| M300688 |
102 |
41.106310 |
3.898127 |
Caecum right |
B12 |
MSEB0009 |
half_ulv2 |
14710.394 |
18826.57 |
4976 |
| M300689 |
94 |
40.781853 |
4.001373 |
Caecum right |
B12 |
MSEB0009 |
half_ulv2 |
14280.268 |
17123.50 |
4976 |
| M300690 |
97 |
40.763262 |
4.104831 |
Caecum right |
B12 |
MSEB0009 |
half_ulv2 |
9132.332 |
19004.86 |
5140 |
| M300691 |
117 |
43.804454 |
4.019294 |
Caecum right |
B12 |
MSEB0009 |
half_ulv2 |
9914.940 |
18812.94 |
5140 |
| M300692 |
105 |
44.986055 |
4.091548 |
Caecum right |
B12 |
MSEB0009 |
half_ulv2 |
12814.906 |
20311.48 |
5140 |
| M300694 |
84 |
37.691549 |
3.890651 |
Caecum right |
B12 |
MSEB0009 |
half_ulv2 |
12365.162 |
19024.05 |
5140 |
| M300695 |
97 |
42.198415 |
3.886696 |
Caecum right |
B12 |
MSEB0009 |
half_ulv2 |
13549.800 |
18825.93 |
5140 |
| M300696 |
103 |
41.230141 |
4.023761 |
Caecum right |
B12 |
MSEB0009 |
half_ulv2 |
12894.764 |
18832.32 |
5140 |
| M300697 |
88 |
40.517297 |
4.047342 |
Caecum right |
B12 |
MSEB0009 |
half_ulv2 |
13465.594 |
19185.00 |
5140 |
| M300698 |
7 |
2.528667 |
1.440155 |
Ileum |
B02 |
MSEB0009 |
full_ulv2 |
NA |
NA |
NA |
| M300699 |
8 |
2.595056 |
1.452254 |
Ileum |
B02 |
MSEB0009 |
full_ulv2 |
NA |
NA |
NA |
| M300700 |
9 |
3.078360 |
1.535261 |
Ileum |
B12 |
MSEB0009 |
full_ulv2 |
NA |
NA |
NA |
| M300701 |
8 |
3.259559 |
1.578356 |
Ileum |
B12 |
MSEB0009 |
full_ulv2 |
NA |
NA |
NA |
| Undeter |
114 |
45.506971 |
4.113590 |
NA |
NA |
NA |
NA |
NA |
NA |
NA |
# Print alpha diversity summary
alpha_diversity %>%
select(richness, neutral, phylogenetic, section, batch, protocol) %>%
group_by(section, batch, protocol) %>%
summarise(richness=mean(richness), neutral=mean(neutral), phylogenetic=mean(phylogenetic)) %>%
tt()
tinytable_cu0fpnau22l88wwxyskl
| section |
batch |
protocol |
richness |
neutral |
phylogenetic |
| Caecum right |
MSEB0006 |
full_ulv2 |
89.50000 |
39.563947 |
3.814879 |
| Caecum right |
MSEB0009 |
full_celero |
83.50000 |
34.570989 |
3.660827 |
| Caecum right |
MSEB0009 |
half_ulv2 |
91.69231 |
38.416403 |
3.912156 |
| Ileum |
MSEB0006 |
full_ulv2 |
3.59375 |
2.222942 |
1.320274 |
| Ileum |
MSEB0009 |
full_ulv2 |
8.00000 |
2.865410 |
1.501506 |
| NA |
NA |
NA |
114.00000 |
45.506971 |
4.113590 |
alpha_diversity %>%
pivot_longer(!c(microsample,section,cryosection,type,buffer,batch,protocol,Xcoord,Ycoord,size), names_to = "metric", values_to = "value") %>%
left_join(quality,by=join_by(microsample==microsample)) %>%
mutate(metric=factor(metric,levels=c("richness","neutral","phylogenetic"))) %>%
ggplot(aes(x=protocol, y=value, color=quality, group=protocol))+
scale_color_gradient(low = "red", high = "green", name = "Quality") +
geom_boxplot(outlier.shape = NA) +
geom_jitter(width=0.2) +
facet_grid(metric ~ section, scales = "free")

alpha_diversity %>%
pivot_longer(!c(microsample,section,cryosection,type,buffer,batch,protocol,Xcoord,Ycoord,size), names_to = "metric", values_to = "value") %>%
left_join(quality,by=join_by(microsample==microsample)) %>%
mutate(metric=factor(metric,levels=c("richness","neutral","phylogenetic"))) %>%
ggplot(aes(x=batch, y=value, color=quality, group=batch))+
scale_color_gradient(low = "red", high = "green", name = "Quality") +
geom_boxplot(outlier.shape = NA) +
geom_jitter(width=0.2) +
facet_grid(metric ~ section, scales = "free")

Unfiltered
#Calculate Hill numbers
richness <- genome_counts %>%
column_to_rownames(var="genome") %>%
select(where(~!all(. == 0))) %>%
hilldiv(.,q=0) %>%
t() %>%
as.data.frame() %>%
rename(richness=1) %>%
rownames_to_column(var="microsample")
neutral <- genome_counts %>%
column_to_rownames(var="genome") %>%
select(where(~!all(. == 0))) %>%
hilldiv(.,q=1) %>%
t() %>%
as.data.frame() %>%
rename(neutral=1) %>%
rownames_to_column(var="microsample")
phylogenetic <- genome_counts %>%
column_to_rownames(var="genome") %>%
select(where(~!all(. == 0))) %>%
hilldiv(.,q=1,tree=genome_tree) %>%
t() %>%
as.data.frame() %>%
rename(phylogenetic=1) %>%
rownames_to_column(var="microsample")
# Merge alpha diversities
alpha_diversity <- richness %>%
full_join(neutral,by=join_by(microsample==microsample)) %>%
full_join(phylogenetic,by=join_by(microsample==microsample)) %>%
left_join(sample_metadata, by=join_by(microsample==microsample))
# Write alpha diversities
alpha_diversity %>% write_tsv("results/alpha_div_unfiltered.tsv")
# Print alpha diversity
alpha_diversity %>%
select(microsample,richness, neutral, phylogenetic, section, buffer, Xcoord, Ycoord, size) %>%
tt()
tinytable_ezyuru4h8o4dt42rvvfy
| microsample |
richness |
neutral |
phylogenetic |
section |
buffer |
Xcoord |
Ycoord |
size |
| M300554 |
252 |
59.048724 |
4.005426 |
Caecum right |
B11 |
74953.325 |
27445.67 |
4976 |
| M300555 |
234 |
29.591689 |
3.136402 |
Caecum right |
B11 |
72020.280 |
33695.14 |
4976 |
| M300556 |
242 |
52.377341 |
3.862228 |
Caecum right |
B11 |
75415.387 |
27819.35 |
4976 |
| M300557 |
252 |
60.880377 |
3.919625 |
Caecum right |
B11 |
76113.477 |
28351.85 |
4976 |
| M300558 |
147 |
16.388623 |
3.084364 |
Caecum right |
B11 |
NA |
NA |
NA |
| M300559 |
252 |
59.602278 |
4.019172 |
Caecum right |
B11 |
76849.228 |
29025.05 |
4976 |
| M300560 |
252 |
58.645287 |
4.181971 |
Caecum right |
B11 |
75971.705 |
29352.86 |
4976 |
| M300561 |
252 |
57.105278 |
4.190661 |
Caecum right |
B11 |
76680.937 |
29558.16 |
4976 |
| M300562 |
252 |
60.378741 |
4.115130 |
Caecum right |
B11 |
74883.318 |
29170.18 |
5140 |
| M300563 |
252 |
59.645294 |
4.072592 |
Caecum right |
B11 |
75220.992 |
29120.51 |
5140 |
| M300564 |
246 |
52.890970 |
4.203353 |
Caecum right |
B11 |
75894.617 |
29134.86 |
5140 |
| M300565 |
48 |
13.113524 |
4.215440 |
Caecum right |
B11 |
72986.812 |
36482.20 |
5140 |
| M300566 |
251 |
58.164898 |
3.882696 |
Caecum right |
B11 |
76922.541 |
29224.45 |
5140 |
| M300567 |
252 |
57.810869 |
4.124295 |
Caecum right |
B11 |
77492.203 |
29097.78 |
5140 |
| M300568 |
40 |
10.638020 |
2.635867 |
Caecum right |
B11 |
NA |
NA |
NA |
| M300569 |
252 |
60.745119 |
4.196834 |
Caecum right |
B11 |
77495.465 |
28977.76 |
5140 |
| M300570 |
252 |
57.723816 |
4.052962 |
Caecum right |
B11 |
74950.841 |
28473.11 |
4815 |
| M300571 |
251 |
56.661744 |
4.017740 |
Caecum right |
B11 |
75619.946 |
28632.40 |
4815 |
| M300572 |
249 |
56.949762 |
4.191364 |
Caecum right |
B11 |
76345.933 |
29031.81 |
4815 |
| M300573 |
178 |
34.564442 |
3.598634 |
Caecum right |
B11 |
74609.411 |
34469.39 |
4815 |
| M300574 |
251 |
57.725467 |
4.082745 |
Caecum right |
B11 |
76920.997 |
29347.99 |
4815 |
| M300575 |
135 |
59.863456 |
4.655632 |
Caecum right |
B11 |
NA |
NA |
NA |
| M300576 |
251 |
57.389815 |
4.083745 |
Caecum right |
B11 |
77104.532 |
29588.79 |
4815 |
| M300577 |
252 |
57.842513 |
4.079376 |
Caecum right |
B11 |
77418.895 |
29907.92 |
4815 |
| M300578 |
252 |
57.743125 |
4.012410 |
Caecum right |
B12 |
76897.212 |
30198.48 |
5140 |
| M300579 |
221 |
38.829262 |
3.357156 |
Caecum right |
B12 |
73304.285 |
36352.33 |
5140 |
| M300580 |
250 |
55.871239 |
4.042301 |
Caecum right |
B12 |
77026.940 |
30039.53 |
5140 |
| M300581 |
252 |
56.693254 |
4.077549 |
Caecum right |
B12 |
77028.597 |
29718.20 |
5140 |
| M300582 |
251 |
55.908533 |
4.078589 |
Caecum right |
B12 |
77019.213 |
29448.24 |
5140 |
| M300583 |
252 |
51.029088 |
4.100996 |
Caecum right |
B12 |
77009.202 |
28923.10 |
5140 |
| M300584 |
252 |
57.684739 |
4.058398 |
Caecum right |
B12 |
77019.413 |
28061.84 |
5140 |
| M300585 |
85 |
36.312174 |
5.379855 |
Caecum right |
B12 |
NA |
NA |
NA |
| M300586 |
48 |
21.091967 |
4.510739 |
Caecum right |
B12 |
73652.539 |
35857.69 |
5141 |
| M300587 |
8 |
3.491849 |
1.592392 |
Caecum right |
B12 |
NA |
NA |
NA |
| M300588 |
252 |
54.764773 |
4.072549 |
Caecum right |
B12 |
75330.017 |
26890.36 |
5141 |
| M300589 |
253 |
54.565428 |
4.052600 |
Caecum right |
B12 |
75862.866 |
27323.96 |
5141 |
| M300590 |
252 |
53.695112 |
4.232105 |
Caecum right |
B12 |
76508.231 |
27653.84 |
5141 |
| M300591 |
193 |
44.669792 |
3.308027 |
Caecum right |
B12 |
76848.926 |
27815.44 |
5141 |
| M300592 |
251 |
52.703789 |
4.157326 |
Caecum right |
B12 |
77351.464 |
28017.27 |
5141 |
| M300593 |
253 |
54.697582 |
4.159239 |
Caecum right |
B12 |
77854.216 |
28261.49 |
5141 |
| M300594 |
252 |
57.267685 |
4.154592 |
Caecum right |
B12 |
75509.650 |
26477.82 |
4976 |
| M300595 |
251 |
49.303188 |
4.159722 |
Caecum right |
B12 |
75650.540 |
26591.91 |
4976 |
| M300596 |
252 |
51.537550 |
4.129928 |
Caecum right |
B12 |
75822.838 |
26598.11 |
4976 |
| M300597 |
251 |
52.894386 |
4.187497 |
Caecum right |
B12 |
76147.102 |
26625.28 |
4976 |
| M300598 |
252 |
54.366506 |
4.127848 |
Caecum right |
B12 |
76899.245 |
26623.52 |
4976 |
| M300599 |
252 |
55.014439 |
4.041644 |
Caecum right |
B12 |
76852.725 |
26643.02 |
4976 |
| M300600 |
37 |
12.471508 |
3.871589 |
Caecum right |
B12 |
NA |
NA |
NA |
| M300601 |
122 |
44.752920 |
6.549661 |
Caecum right |
B12 |
72982.582 |
21722.53 |
4976 |
| M300602 |
195 |
3.770399 |
1.526286 |
Ileum |
B11 |
104424.700 |
42749.48 |
5140 |
| M300603 |
172 |
3.443781 |
1.761321 |
Ileum |
B11 |
104606.900 |
42459.54 |
5140 |
| M300604 |
54 |
11.488595 |
3.430860 |
Ileum |
B11 |
101758.400 |
36668.70 |
5140 |
| M300605 |
154 |
3.468041 |
1.580848 |
Ileum |
B11 |
104954.500 |
42730.89 |
5140 |
| M300606 |
231 |
42.312840 |
4.055184 |
Ileum |
B11 |
105122.500 |
42666.74 |
5140 |
| M300607 |
25 |
4.742713 |
1.877699 |
Ileum |
B11 |
NA |
NA |
NA |
| M300608 |
180 |
3.093547 |
1.514223 |
Ileum |
B11 |
105262.700 |
42589.77 |
5140 |
| M300609 |
207 |
3.586403 |
1.515176 |
Ileum |
B11 |
105328.900 |
42703.60 |
5140 |
| M300610 |
193 |
3.434464 |
1.521143 |
Ileum |
B11 |
105102.400 |
41497.10 |
4976 |
| M300611 |
75 |
4.120703 |
1.781889 |
Ileum |
B11 |
105146.000 |
41596.22 |
4976 |
| M300612 |
186 |
3.576177 |
1.512044 |
Ileum |
B11 |
105281.000 |
41702.52 |
4976 |
| M300613 |
71 |
2.227148 |
1.360170 |
Ileum |
B11 |
105408.300 |
41533.66 |
4976 |
| M300614 |
51 |
13.957408 |
4.473484 |
Ileum |
B11 |
101928.600 |
37181.60 |
4976 |
| M300615 |
76 |
33.344988 |
4.963147 |
Ileum |
B11 |
NA |
NA |
NA |
| M300616 |
174 |
1.845652 |
1.249203 |
Ileum |
B11 |
105595.700 |
41999.37 |
4976 |
| M300617 |
236 |
5.332503 |
1.984855 |
Ileum |
B11 |
105983.000 |
42106.21 |
4976 |
| M300618 |
56 |
8.503252 |
2.626672 |
Ileum |
B11 |
101861.400 |
37375.71 |
5306 |
| M300619 |
175 |
2.550470 |
1.410755 |
Ileum |
B11 |
106845.700 |
41525.80 |
5306 |
| M300620 |
28 |
7.640770 |
2.905044 |
Ileum |
B11 |
NA |
NA |
NA |
| M300621 |
119 |
12.148781 |
3.349201 |
Ileum |
B11 |
107360.500 |
41744.06 |
5306 |
| M300622 |
221 |
4.591257 |
1.766175 |
Ileum |
B11 |
107262.300 |
42133.87 |
5306 |
| M300623 |
160 |
3.966379 |
1.799967 |
Ileum |
B11 |
107820.600 |
41925.02 |
5306 |
| M300624 |
115 |
1.651694 |
1.232074 |
Ileum |
B11 |
107233.500 |
41764.35 |
5306 |
| M300625 |
144 |
5.388601 |
2.320102 |
Ileum |
B11 |
107258.100 |
42448.02 |
5306 |
| M300626 |
41 |
8.538645 |
2.863586 |
Ileum |
B12 |
NA |
NA |
NA |
| M300627 |
144 |
3.518088 |
1.512361 |
Ileum |
B12 |
108112.000 |
45420.81 |
4815 |
| M300628 |
175 |
3.173885 |
1.607903 |
Ileum |
B12 |
108221.600 |
45346.45 |
4815 |
| M300629 |
182 |
2.393480 |
1.450458 |
Ileum |
B12 |
108085.500 |
45636.13 |
4815 |
| M300630 |
182 |
2.332205 |
1.406259 |
Ileum |
B12 |
108093.700 |
45848.93 |
4815 |
| M300631 |
208 |
4.627633 |
1.966486 |
Ileum |
B12 |
107697.500 |
45704.29 |
4815 |
| M300632 |
139 |
31.364862 |
4.012416 |
Ileum |
B12 |
102872.400 |
38456.93 |
4815 |
| M300633 |
216 |
2.511084 |
1.495177 |
Ileum |
B12 |
107727.500 |
45487.09 |
4815 |
| M300634 |
213 |
3.122181 |
1.540972 |
Ileum |
B12 |
106635.900 |
42106.55 |
5384 |
| M300635 |
30 |
5.405679 |
2.215422 |
Ileum |
B12 |
NA |
NA |
NA |
| M300636 |
204 |
3.509144 |
1.743930 |
Ileum |
B12 |
106545.500 |
42220.70 |
5384 |
| M300637 |
51 |
2.910588 |
1.509677 |
Ileum |
B12 |
106948.100 |
42956.50 |
5384 |
| M300638 |
203 |
3.460643 |
1.642359 |
Ileum |
B12 |
106647.000 |
42288.86 |
5384 |
| M300639 |
224 |
2.990724 |
1.567194 |
Ileum |
B12 |
106800.500 |
41821.88 |
5384 |
| M300640 |
139 |
2.600750 |
1.476414 |
Ileum |
B12 |
107052.700 |
42525.49 |
5384 |
| M300641 |
98 |
27.021534 |
5.575144 |
Ileum |
B12 |
103203.400 |
38334.96 |
5384 |
| M300642 |
72 |
2.706444 |
1.584137 |
Ileum |
B12 |
108030.700 |
43599.50 |
4976 |
| M300643 |
16 |
5.123028 |
1.769523 |
Ileum |
B12 |
101876.900 |
39000.58 |
4976 |
| M300644 |
225 |
1.815382 |
1.244790 |
Ileum |
B12 |
NA |
NA |
NA |
| M300645 |
192 |
1.687109 |
1.278009 |
Ileum |
B12 |
107988.200 |
43509.47 |
4976 |
| M300646 |
64 |
13.841432 |
3.496467 |
Ileum |
B12 |
NA |
NA |
NA |
| M300647 |
201 |
3.557171 |
1.509236 |
Ileum |
B12 |
107969.500 |
43138.84 |
4976 |
| M300648 |
198 |
2.029309 |
1.315127 |
Ileum |
B12 |
107883.700 |
43169.50 |
4976 |
| M300649 |
74 |
4.148091 |
1.828161 |
Ileum |
B12 |
107984.200 |
43047.52 |
4976 |
| M300650 |
90 |
25.547686 |
5.490960 |
Caecum right |
B12 |
13017.480 |
NA |
NA |
| M300651 |
252 |
60.334462 |
4.037827 |
Caecum right |
B12 |
11906.706 |
17302.78 |
5140 |
| M300652 |
252 |
55.706583 |
4.230868 |
Caecum right |
B12 |
14050.460 |
17001.92 |
5140 |
| M300653 |
205 |
23.115889 |
2.885944 |
Caecum right |
B12 |
15132.646 |
18629.72 |
5140 |
| M300654 |
252 |
49.719436 |
3.958627 |
Caecum right |
B12 |
14807.470 |
19475.98 |
5140 |
| M300655 |
66 |
11.835013 |
3.758529 |
Caecum right |
B12 |
12921.636 |
17630.90 |
5140 |
| M300656 |
237 |
51.627998 |
3.879326 |
Caecum right |
B12 |
15095.242 |
18655.46 |
5140 |
| M300657 |
249 |
40.393213 |
4.019623 |
Caecum right |
B12 |
15154.326 |
19081.92 |
5140 |
| M300658 |
252 |
55.646080 |
4.151520 |
Caecum right |
B12 |
9192.814 |
19234.39 |
4976 |
| M300659 |
252 |
52.072344 |
4.069240 |
Caecum right |
B12 |
12511.076 |
19365.33 |
4976 |
| M300660 |
76 |
5.499699 |
2.285934 |
Caecum right |
B12 |
11930.670 |
19818.58 |
4976 |
| M300661 |
253 |
51.583910 |
4.013095 |
Caecum right |
B12 |
11699.514 |
20259.00 |
4976 |
| M300662 |
251 |
56.603450 |
3.916391 |
Caecum right |
B12 |
13804.910 |
20094.72 |
4976 |
| M300663 |
97 |
10.308725 |
4.266069 |
Caecum right |
B12 |
NA |
NA |
NA |
| M300664 |
249 |
30.493582 |
3.840296 |
Caecum right |
B12 |
12513.988 |
21896.24 |
4976 |
| M300665 |
240 |
19.254617 |
3.317076 |
Caecum right |
B12 |
9669.578 |
19330.82 |
4976 |
| M300666 |
252 |
53.743891 |
4.080995 |
Caecum right |
B12 |
10924.656 |
21602.49 |
5384 |
| M300667 |
73 |
21.078963 |
5.788265 |
Caecum right |
B12 |
NA |
NA |
NA |
| M300668 |
252 |
50.277071 |
4.072904 |
Caecum right |
B12 |
14208.788 |
22187.84 |
5384 |
| M300669 |
252 |
52.995755 |
4.195787 |
Caecum right |
B12 |
13658.990 |
21278.18 |
5384 |
| M300670 |
249 |
54.520367 |
4.020114 |
Caecum right |
B12 |
15752.910 |
20908.01 |
5384 |
| M300671 |
251 |
52.121850 |
4.170802 |
Caecum right |
B12 |
13086.410 |
21703.25 |
5384 |
| M300672 |
252 |
53.386952 |
3.983508 |
Caecum right |
B12 |
13311.294 |
20916.06 |
5384 |
| M300673 |
251 |
50.112142 |
4.146929 |
Caecum right |
B12 |
14520.766 |
22307.33 |
5384 |
| M300674 |
252 |
56.789427 |
4.028199 |
Caecum right |
B12 |
12054.270 |
23154.78 |
5051 |
| M300675 |
252 |
55.626538 |
4.026539 |
Caecum right |
B12 |
13501.846 |
20960.88 |
5051 |
| M300676 |
250 |
52.022526 |
4.150433 |
Caecum right |
B12 |
14952.726 |
23717.40 |
5051 |
| M300677 |
247 |
51.570297 |
3.979858 |
Caecum right |
B12 |
12773.380 |
21535.84 |
5051 |
| M300678 |
253 |
53.265316 |
4.073765 |
Caecum right |
B12 |
12504.528 |
21793.47 |
5051 |
| M300679 |
252 |
52.843053 |
4.090399 |
Caecum right |
B12 |
12589.016 |
20536.83 |
5051 |
| M300680 |
252 |
56.085699 |
4.115161 |
Caecum right |
B12 |
13215.834 |
22405.85 |
5051 |
| M300681 |
199 |
15.133302 |
3.203389 |
Caecum right |
B12 |
NA |
NA |
NA |
| M300682 |
237 |
49.016763 |
4.129097 |
Caecum right |
B12 |
14464.852 |
18168.78 |
4976 |
| M300683 |
252 |
52.766786 |
4.190538 |
Caecum right |
B12 |
15660.538 |
17029.20 |
4976 |
| M300684 |
251 |
49.976106 |
4.087444 |
Caecum right |
B12 |
13001.740 |
18200.66 |
4976 |
| M300685 |
222 |
32.549462 |
4.768086 |
Caecum right |
B12 |
NA |
NA |
NA |
| M300686 |
215 |
58.246778 |
3.986024 |
Caecum right |
B12 |
14173.260 |
17741.15 |
4976 |
| M300687 |
251 |
54.586232 |
4.091225 |
Caecum right |
B12 |
14317.052 |
18439.38 |
4976 |
| M300688 |
251 |
53.413916 |
4.010619 |
Caecum right |
B12 |
14710.394 |
18826.57 |
4976 |
| M300689 |
252 |
54.070423 |
4.127761 |
Caecum right |
B12 |
14280.268 |
17123.50 |
4976 |
| M300690 |
252 |
53.782859 |
4.233271 |
Caecum right |
B12 |
9132.332 |
19004.86 |
5140 |
| M300691 |
252 |
54.125918 |
4.099929 |
Caecum right |
B12 |
9914.940 |
18812.94 |
5140 |
| M300692 |
252 |
57.228981 |
4.188129 |
Caecum right |
B12 |
12814.906 |
20311.48 |
5140 |
| M300693 |
58 |
23.416149 |
5.412036 |
Caecum right |
B12 |
NA |
NA |
NA |
| M300694 |
251 |
51.989711 |
4.068597 |
Caecum right |
B12 |
12365.162 |
19024.05 |
5140 |
| M300695 |
252 |
55.251650 |
4.033557 |
Caecum right |
B12 |
13549.800 |
18825.93 |
5140 |
| M300696 |
251 |
53.015006 |
4.124372 |
Caecum right |
B12 |
12894.764 |
18832.32 |
5140 |
| M300697 |
252 |
55.034448 |
4.188927 |
Caecum right |
B12 |
13465.594 |
19185.00 |
5140 |
| M300698 |
239 |
2.871161 |
1.498583 |
Ileum |
B02 |
NA |
NA |
NA |
| M300699 |
240 |
2.908721 |
1.497934 |
Ileum |
B02 |
NA |
NA |
NA |
| M300700 |
244 |
3.598605 |
1.600967 |
Ileum |
B12 |
NA |
NA |
NA |
| M300701 |
243 |
3.910067 |
1.663592 |
Ileum |
B12 |
NA |
NA |
NA |
| M300702 |
8 |
3.007004 |
1.354425 |
Caecum right |
NA |
NA |
NA |
NA |
| M300703 |
6 |
2.681496 |
1.290717 |
Caecum right |
NA |
NA |
NA |
NA |
| Undeter |
253 |
56.603367 |
4.191806 |
NA |
NA |
NA |
NA |
NA |
# Print alpha diversity summary
alpha_diversity %>%
select(richness, neutral, phylogenetic, section, buffer) %>%
group_by(section, buffer) %>%
summarise(richness=mean(richness), neutral=mean(neutral), phylogenetic=mean(phylogenetic)) %>%
tt()
tinytable_ulojsdrcy59t2x94oiw6
| section |
buffer |
richness |
neutral |
phylogenetic |
| Caecum right |
B11 |
220.6250 |
50.239502 |
3.942011 |
| Caecum right |
B12 |
219.5417 |
46.071485 |
4.088926 |
| Caecum right |
NA |
7.0000 |
2.844250 |
1.322571 |
| Ileum |
B02 |
239.5000 |
2.889941 |
1.498259 |
| Ileum |
B11 |
137.4167 |
7.924440 |
2.229897 |
| Ileum |
B12 |
153.0000 |
5.842222 |
1.956760 |
| NA |
NA |
253.0000 |
56.603367 |
4.191806 |
alpha_diversity %>%
pivot_longer(!c(microsample,section,cryosection,type,buffer,batch,protocol,Xcoord,Ycoord,size), names_to = "metric", values_to = "value") %>%
left_join(quality,by=join_by(microsample==microsample)) %>%
mutate(metric=factor(metric,levels=c("richness","neutral","phylogenetic"))) %>%
ggplot(aes(x=protocol, y=value, color=quality, group=protocol))+
scale_color_gradient(low = "red", high = "green", name = "Quality") +
geom_boxplot(outlier.shape = NA) +
geom_jitter(width=0.2) +
facet_grid(metric ~ section, scales = "free")

alpha_diversity %>%
pivot_longer(!c(microsample,section,cryosection,type,buffer,batch,protocol,Xcoord,Ycoord,size), names_to = "metric", values_to = "value") %>%
left_join(quality,by=join_by(microsample==microsample)) %>%
mutate(metric=factor(metric,levels=c("richness","neutral","phylogenetic"))) %>%
ggplot(aes(x=batch, y=value, color=quality, group=batch))+
scale_color_gradient(low = "red", high = "green", name = "Quality") +
geom_boxplot(outlier.shape = NA) +
geom_jitter(width=0.2) +
facet_grid(metric ~ section, scales = "free")
